Lecture 16. Prokaryotes, Eukaryotes, and the Tree of Life, rRNA, Constructing Trees

reading: Chapters 3, 5

Lecture 16. Prokaryotes, Eukaryotes, and the Tree of Life, rRNA, Constructing Trees.

Textbook General Morphology 1866 Traces all of life to Moneren (Monera).Linear progress from Monera to Man.

Ernst Haeckel

QuickTime™ and aTIFF (Uncompressed) decompressor

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Yet another version of Haeckel’s tree of life

All eukaryotes descended from prokaryotes, culminating in man.

Prokaryotes not all that interesting.

Zuckerkandl & Pauling

Pauling: 1954 Nobel Prize,nature of the chemical bond

Series of papers in 1962-1965:

Mutations form the basis for disease.Disease has a molecular basis.Studying diseases that involve different forms of hemoglobin.

Showed that:a. if you knew the genetic code, you could trace the mutations

that caused diseaseb. there is buried history in protein (or gene) sequences (hold information)c. approximate time of the existence of an ancestral sequenced. can infer the probable sequence of the ancestor (AACGTTC)e. can infer “the lines of descent along which given changes in amino-

acid sequence occurred”

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Thermus thermophilus GAC-ACGUGGU-AUCCUGUCU-GAAUAU-GGGGGG--ACCA-UCC-U-CCA-AG-GCUA-AAUAC-UC-C-UGSynechocystis PCC 6301 GAC-ACGUGAA-AUCCUGUCU-GAAGAU-GGGGGG--ACCA-UCC-U-CCA-AG-GCUA-AAUAC-UC-G-UGMicrococcus luteus GAC-ACGUGAA-AUCCUGUCU-GAAGAU-CGGGGG--ACCA-CCC-C-CGA-AG-GCUA-AGUAC-UC-C-UUFlexibacterium sp. GAC-ACGUGAA-AUCCUGUCU-GAACGU-GGGGGG--ACCA-CCC-U-CCA-AG-GCUA-AGUAC-UC-C-UUAgrobacterium tumefaciens GAC-ACGUGAA-AUCCUGUUC-GAACAU-GGGGAG--ACCA-CUC-U-CCA-AG-CCUA-AGUAC-UC-G-UGEscherichia coli GAC-ACGUGGU-AUCCUGUCU-GAAUAU-GGGGGG--ACCA-UCC-U-CCA-AG-GCUA-AAUAC-UC-C-UGPseudomonas cepacia GAC-ACGUGAA-AUCCUGUCU-GAAGAU-GGGGGG--ACCA-UCC-U-CCA-AG-GCUA-AAUAC-UC-G-UGAquifex aeolicus GAC-ACGUGAA-AUCCUGUCU-GAAGAU-CGGGGG--ACCA-CCC-C-CGA-AG-GCUA-AGUAC-UC-C-UUChloroflexus aurantiacus GAC-ACGUGAA-AUCCUGUCU-GAACGU-GGGGGG--ACCA-CCC-U-CCA-AG-GCUA-AGUAC-UC-C-UU

treereconstruction/inferencealgorithm

DNA extraction

clone

sequence

cells/culture

time

Overall Scheme for Constructing a Phylogenetic Tree

phylogeny -development of a raceor species

Example How to Construct a Phylogenetic Tree

Count the number ofdifferences. Correct for

multiple mutations.

Construct a Tree that Best Explains the Distances Observed

1. chose which taxa2. tabulate traits3. identify synapomorphies

= shared derived traits4. build up a cladogram

= tree showing evolutionary relationships

good introductory resource:www.ucmp.berkeley.edu

TABLE 2 limbs scales amniote feathers hair placenta bloodfrog 4 N N N N N Coldalligator 4 Y Y N N N Coldduck 4 Y Y Y N N Warmcat 4 N Y N Y Y Warmopossum 4 N Y N Y N Warm

Can also Build a Tree using Cladistics

cladistics - reconstructing trees usingshared, derived traits

The Importance of Having A Phylogenetic Tree





The Importance of Having A Phylogenetic Tree, cont.

Tree of Life

Constructed by aligning a gene sequence common to all organisms.Common gene: ribosomal RNA gene.Three major lineages - these are called domains.Root is where the last common ancestor gave rise to the three domains.Root is placed at the base of the bacterial domain.

Ribosome

Synthesizes Proteins in the CellLarge complex made of RNA and small proteinsRNA catalyzes the reaction to make proteinsRNAs called ribosomal RNAs

Archaea are more closely related to Eukaryotes than to Bacteria

At first this was a big surprise - expected Bacteria and Archaea to be more similar to the exclusion of Eukaryotes

1989: Rooting the Tree of Life

three studies:Gogarten et al. ATPasesIwabe et al. tRNA synthetasesBaldauf et al. elongation factors

The Bacterial Domain

At least 18 divisions - major lineages.Some divisions have never been cultured!Some have unique characteristics (e.g., the Cyanobacteria).Most lack unique characteristics.One major group Proteobacteria - have a large variety of different

physiologies

Bacterial tree is notwell resolved atpresent

The Bacterial Domain, cont.

Early lineages are hyperthermophiles.Deinococcus branches somewhat deep.E. coli is a member of the Proteobacteria, branches late.Cyanobacteria also branch late.Bacillus & Clostridium members of the Low G+C Gram Positive Bacteria.Are several lineages of photosynthetic phyla.

Are Five Phyla ContainPhotosynthetic Taxa:Green Non-Sulfur BacteriaGreen Sulfur BacteriaCyanobacteriaLow G+C Gram Positives (Heliobacillus)Proteobacteria

Key Characteristics of Bacteria

1. Cell walls made of a similar polymer (peptidoglycan)2. Lipids are made of similar compounds (fatty acids with ester linkages)3. RNA polymerase (enzyme that makes mRNA copies of genes)

made of 4 different proteins (’)4. Signature sequences tell RNA polymerase where to start making

RNA 5. All proteins begin with a modified amino acid formyl-Methionine

The Archaeal Domain

Two major well-studied phyla are Euryarchaeota and Crenarchaeota.Two new phyla are Korarchaeota (no pure cultures yet) and

Nanoarchaeota (is a symbiont of a Crenarchaeote). Not clear where these lineages branch.

Most of the early branches are hyperthermophilic.

Obsidian Pool, Yellowstone,home of Korarchaeota

Crenarchaeota

All cultured species are hyperthermophilic.Many inhabit “extreme environments”:hyperthermophiles- very high T lovingthermoacidophiles - high T acid lovingMany have short branches - evolve slowly.

(should, in principle, be good models for early life on Earth)Great deal of uncultured mesophiles (moderate T loving) everywhere - 30% of

biomass in the open oceans.Mesophiles have long branches - evolving more rapidly.Mesophilic lineages are peripheral.



red cells are Archaeagreen are Bacteria

marine hydrothermal vent

terrestrial acidic hot spring

Euryarchaeota

Physiologically diverse group.Inhabit many extreme environments:

acidophiles- acid lovingthermoacidophileshalophiles- salt lovingalkaliphiles- alkaline lovinghyperthermophiles

Many lineages are methanogens - generate methane,are strict anaerobes (can only grow without O2)

Methanogens found in diverse habitats:swamps, deep-sea hydrothermal vents, animal intestines, cow rumen, rice paddies,oil wells

Key Characteristics of Archaea

1. Cell walls are different than bacteria (pseudopeptidoglycan)2. Lipids different from bacteria (isoprenoids with ether linkages)3. RNA polymerase more complex than bacteria -

8 or more proteins (eukaryotes have 8-10)4. RNA polymerase needs “help” from other proteins to begin

making mRNA copies of genes (called transcription factors -are similar to eukaryotes)

5. Signature sequences also tell RNA polymerase where to start making RNA, but are unique (TATA boxes - similar to eukaryotes)

6. All proteins begin with the regular amino acid Methionine7. The number of ribosomal proteins are different from bacteria.

Archaea and Bacteria Share Many Characteristics

1. Genes are often linked together in the chromosome2. Have circular chromosomes (eukaryotes have linear chromosomes)3. Genomes are small (eukaryote genomes are huge)4. Both have ribosomes that are small (eukaryotes have larger ribosomes)5. Both metabolically diverse (eukaryotes are not)6. Lack nucleus

…. many more ….

EukaryotesProkaryotes- lack nucleus/nucleiEukaryote (“true nucleus”)are much more complexDNA containing organelles (“little organs”)

nucleusmitochondrion - respirationchloroplast - photosynthesis }were once free-living prokaryotes

often have multiple chromosomes(linear chromosomes)lots more geneslots of “junk DNA” in their genes

Eukaryotes are Typically Larger than Prokaryotes

reading: none

Lecture 17. Why Do You Need to Construct a Tree for Prokaryotes? Trees as

Frameworks



Cassini Spacecraft found older terrainsand major fractures on moon Enceladus

Course crystalline ice which will degrade overtime.

Must be < 1000 years old!Organic compounds found in the fractures.Must be heated - required T > 100K (-173˚C)Erupting jets of water observed.Cause of eruptions not known….



Mystery of Enceladus



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Lecture 16. Prokaryotes, Eukaryotes, and the Tree of Life, rRNA, Constructing Trees